Re: [AMBER] Restraint problem

From: Fernando Martín García <>
Date: Fri, 10 Aug 2012 11:59:43 +0200

 You are right. We were having a little misunderstood with our system
 and iwrap. Our system and restrains works fine with iwrap=0.

 Thanks for the help.


 On Wed, 8 Aug 2012 09:30:05 -0400, case wrote:
> On Wed, Aug 08, 2012, Fernando Martín García wrote:
>> I have a "technical" problem with a distance restraint. I'm working
>> with a protein with a 12 angs. TIP3 box. The simulation time is 30
>> ns.
>> After 20 ns, a small part of the protein is out of the box. The
>> problem
>> is that one of the residues out of the box has a restrain with one
>> residue in the part of the protein inside the water box, so the
>> value
>> changes, what it causes a high restraint value. Is there any
>> solution
>> for this?
> I'm confused by this description. Is the restraint between two atoms
> in the
> same polypeptide chain? If so, the distance should be unaffected by
> wrapping
> or imaging, and have nothing to do with being "outside of the box" or
> not.
> In this case, you need to look more carefully into what might be
> causing the
> problem.
> (As an aside: protein residues are never really "outside the box";
> the may
> appear to be that way visually, but periodic images of solvent
> molecules are
> acutally nearby and used in all energy and force calculations.)
> If the restraint is between two different "molecules" (e.g.
> polypeptide
> chains), then you need to set iwrap=0 to prevent wrapping from
> suddenly
> changing the distance involved in the restraint. In that case, you
> may
> need to occasionally use cpptraj to center and image the restart file
> to
> make things more compact.
> ...good luck....dac
> _______________________________________________
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  Fernando Martín García
  Molecular Modelling Group - Lab 312.1
  Molecular Biology Center "Severo Ochoa"
  UAM University. Cantoblanco, 28049 Madrid. Spain.
  TEL: (+34) 91-196-4662 FAX: (+34) 91-196-4420
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Received on Fri Aug 10 2012 - 03:30:03 PDT
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